OpenRaiser/Intern-Atlas huggingface dataset:
Uncovering Intervention Opportunities for Suicide Prevention with Language Model Assistants
Venue: arXiv cs.CY 2025
Year: 2025

Warning: This paper discusses topics of suicide and suicidal ideation, which may be distressing to some readers. The National Violent Death Reporting System (NVDRS) documents information about suicides in the United States, including free text narratives (e.g., circumstances surrounding a suicide). In a demanding public health data pipeline, annotators manually extract structured information from death investigation records following extensive guidelines developed painstakingly by experts. In this work, we facilitate data-driven insights from the NVDRS data to support the development of novel suicide interventions by investigating the value of language models (LMs) as efficient assistants to these (a) data annotators and (b) experts. We find that LM predictions match existing data annotations about 85% of the time across 50 NVDRS variables. In the cases where the LM disagrees with existing annotations, expert review reveals that LM assistants can surface annotation discrepancies 38% of the time. Finally, we introduce a human-in-the-loop algorithm to assist experts in efficiently building and refining guidelines for annotating new variables by allowing them to focus only on providing feedback for incorrect LM predictions. We apply our algorithm to a real-world case study for a new variable that characterizes victim interactions with lawyers and demonstrate that it achieves comparable annotation quality with a laborious manual approach. Our findings provide evidence that LMs can serve as effective assistants to public health researchers who handle sensitive data in high-stakes scenarios.
Enhancing Chemical Explainability Through Counterfactual Masking
Venue: arXiv cs.LG 2025
Year: 2025

Molecular property prediction is a crucial task that guides the design of new compounds, including drugs and materials. While explainable artificial intelligence methods aim to scrutinize model predictions by identifying influential molecular substructures, many existing approaches rely on masking strategies that remove either atoms or atom-level features to assess importance via fidelity metrics. These methods, however, often fail to adhere to the underlying molecular distribution and thus yield unintuitive explanations. In this work, we propose counterfactual masking, a novel framework that replaces masked substructures with chemically reasonable fragments sampled from generative models trained to complete molecular graphs. Rather than evaluating masked predictions against implausible zeroed-out baselines, we assess them relative to counterfactual molecules drawn from the data distribution. Our method offers two key benefits: (1) molecular realism underpinning robust and distribution-consistent explanations, and (2) meaningful counterfactuals that directly indicate how structural modifications may affect predicted properties. We demonstrate that counterfactual masking is well-suited for benchmarking model explainers and yields more actionable insights across multiple datasets and property prediction tasks. Our approach bridges the gap between explainability and molecular design, offering a principled and generative path toward explainable machine learning in chemistry.
Sparse Autoencoders for Low-$N$ Protein Function Prediction and Design
Venue: arXiv cs.LG 2025
Year: 2025

Predicting protein function from amino acid sequence remains a central challenge in data-scarce (low-$N$) regimes, limiting machine learning-guided protein design when only small amounts of assay-labeled sequence-function data are available. Protein language models (pLMs) have advanced the field by providing evolutionary-informed embeddings and sparse autoencoders (SAEs) have enabled decomposition of these embeddings into interpretable latent variables that capture structural and functional features. However, the effectiveness of SAEs for low-$N$ function prediction and protein design has not been systematically studied. Herein, we evaluate SAEs trained on fine-tuned ESM2 embeddings across diverse fitness extrapolation and protein engineering tasks. We show that SAEs, with as few as 24 sequences, consistently outperform or compete with their ESM2 baselines in fitness prediction, indicating that their sparse latent space encodes compact and biologically meaningful representations that generalize more effectively from limited data. Moreover, steering predictive latents exploits biological motifs in pLM representations, yielding top-fitness variants in 83% of cases compared to designing with ESM2 alone.
Brook-2PL: Tolerating High Contention Workloads with A Deadlock-Free Two-Phase Locking Protocol
Venue: arXiv cs.DB 2025
Year: 2025

The problem of hotspots remains a critical challenge in high-contention workloads for concurrency control (CC) protocols. Traditional concurrency control approaches encounter significant difficulties under high contention, resulting in excessive transaction aborts and deadlocks. In this paper, we propose Brook-2PL, a novel two-phase locking (2PL) protocol that (1) introduces SLW-Graph for deadlock-free transaction execution, and (2) proposes partial transaction chopping for early lock release. Previous methods suffer from transaction aborts that lead to wasted work and can further burden the system due to their cascading effects. Brook-2PL addresses this limitation by statically analyzing a new graph-based dependency structure called SLW-Graph, enabling deadlock-free two-phase locking through predetermined lock acquisition. Brook-2PL also reduces contention by enabling early lock release using partial transaction chopping and static transaction analysis. We overcome the inherent limitations of traditional transaction chopping by providing a more flexible chopping method. Evaluation using both our synthetic online game store workload and the TPC-C benchmark shows that Brook-2PL significantly outperforms state-of-the-art CC protocols. Brook-2PL achieves an average speed-up of 2.86x while reducing tail latency (p95) by 48% in the TPC-C benchmark.
Portable Silent Room: Exploring VR Design for Anxiety and Emotion Regulation for Neurodivergent Women and Non-Binary Individuals
Venue: arXiv cs.HC 2025
Year: 2025

Neurodivergent individuals, particularly those with Autism and Attention Deficit Hyperactivity Disorder (ADHD), frequently experience anxiety, panic attacks, meltdowns, and emotional dysregulation due to societal pressures and inadequate accommodations. These challenges are especially pronounced for neurodivergent women and non-binary individuals navigating intersecting barriers of neurological differences and gender expectations. This research investigates virtual reality (VR) as a portable safe space for emotional regulation, addressing challenges of sensory overload and motion sickness while enhancing relaxation capabilities. Our mixed-methods approach included an online survey (N=223) and an ideation workshop (N=32), which provided key design elements for creating effective calming VR environments. Based on these findings, we developed and iteratively tested VR prototypes with neurodivergent women and non-binary participants (N=12), leading to a final version offering enhanced adaptability to individual sensory needs. This final prototype underwent a comprehensive evaluation with 25 neurodivergent participants to assess its effectiveness as a regulatory tool. This research contributes to the development of inclusive, adaptive VR environments that function as personalized "portable silent rooms" offering neurodivergent individuals on-demand access to sensory regulation regardless of physical location.
eSkinHealth: A Multimodal Dataset for Neglected Tropical Skin Diseases
Venue: arXiv cs.AI 2025
Year: 2025

Skin Neglected Tropical Diseases (NTDs) impose severe health and socioeconomic burdens in impoverished tropical communities. Yet, advancements in AI-driven diagnostic support are hindered by data scarcity, particularly for underrepresented populations and rare manifestations of NTDs. Existing dermatological datasets often lack the demographic and disease spectrum crucial for developing reliable recognition models of NTDs. To address this, we introduce eSkinHealth, a novel dermatological dataset collected on-site in Côte d'Ivoire and Ghana. Specifically, eSkinHealth contains 5,623 images from 1,639 cases and encompasses 47 skin diseases, focusing uniquely on skin NTDs and rare conditions among West African populations. We further propose an AI-expert collaboration paradigm to implement foundation language and segmentation models for efficient generation of multimodal annotations, under dermatologists' guidance. In addition to patient metadata and diagnosis labels, eSkinHealth also includes semantic lesion masks, instance-specific visual captions, and clinical concepts. Overall, our work provides a valuable new resource and a scalable annotation framework, aiming to catalyze the development of more equitable, accurate, and interpretable AI tools for global dermatology.
Optimal $(α,β)$-Dense Subgraph Search in Bipartite Graphs
Venue: arXiv cs.DB 2025
Year: 2025

Dense subgraph search in bipartite graphs is a fundamental problem in graph analysis, with wide-ranging applications in fraud detection, recommendation systems, and social network analysis. The recently proposed $(α, β)$-dense subgraph model has demonstrated superior capability in capturing the intrinsic density structure of bipartite graphs compared to existing alternatives. However, despite its modeling advantages, the $(α, β)$-dense subgraph model lacks efficient support for query processing and dynamic updates, limiting its practical utility in large-scale applications. To address these limitations, we propose BD-Index, a novel index that answers $(α, β)$-dense subgraph queries in optimal time while using only linear space $O(|E|)$, making it well-suited for real-world applications requiring both fast query processing and low memory consumption. We further develop two complementary maintenance strategies for dynamic bipartite graphs to support efficient updates to the BD-Index. The space-efficient strategy updates the index in time complexity of $O(p \cdot |E|^{1.5})$ per edge insertion or deletion, while maintaining a low space cost of $O(|E|)$ (the same as the index itself), where $p$ is typically a small constant in real-world graphs. In contrast, the time-efficient strategy significantly reduces the update time to $O(p \cdot |E|)$ per edge update by maintaining auxiliary orientation structures, at the cost of increased memory usage up to $O(p \cdot |E|)$. These two strategies provide flexible trade-offs between maintenance efficiency and memory usage, enabling BD-Index to adapt to diverse application requirements. Extensive experiments on 10 large-scale real-world datasets demonstrate high efficiency and scalability of our proposed solutions.
Investigating Document Type, Language, Publication Year, and Author Count Discrepancies Between OpenAlex and Web of Science
Venue: arXiv cs.DL 2025
Year: 2025

Bibliometrics, whether used for research or research evaluation, relies on large multidisciplinary databases of research outputs and citation indices. The Web of Science (WoS) was the main supporting infrastructure of the field for more than 30 years until several new competitors emerged. OpenAlex, a bibliographic database launched in 2022, has distinguished itself for its openness and extensive coverage. While OpenAlex may reduce or eliminate barriers to accessing bibliometric data, one of the concerns that hinders its broader adoption for research and research evaluation is the quality of its metadata. This study aims to assess metadata quality in OpenAlex and WoS, focusing on document type, publication year, language, and number of authors. By addressing discrepancies and misattributions in metadata, this research seeks to enhance awareness of data quality issues that could impact bibliometric research and evaluation outcomes.
OwlCap: Harmonizing Motion-Detail for Video Captioning via HMD-270K and Caption Set Equivalence Reward
Venue: arXiv cs.CV 2025
Year: 2025

Video captioning aims to generate comprehensive and coherent descriptions of the video content, contributing to the advancement of both video understanding and generation. However, existing methods often suffer from motion-detail imbalance, as models tend to overemphasize one aspect while neglecting the other. This imbalance results in incomplete captions, which in turn leads to a lack of consistency in video understanding and generation. To address this issue, we propose solutions from two aspects: 1) Data aspect: We constructed the Harmonizing Motion-Detail 270K (HMD-270K) dataset through a two-stage pipeline: Motion-Detail Fusion (MDF) and Fine-Grained Examination (FGE). 2) Optimization aspect: We introduce the Caption Set Equivalence Reward (CSER) based on Group Relative Policy Optimization (GRPO). CSER enhances completeness and accuracy in capturing both motion and details through unit-to-set matching and bidirectional validation. Based on the HMD-270K supervised fine-tuning and GRPO post-training with CSER, we developed OwlCap, a powerful video captioning multi-modal large language model (MLLM) with motion-detail balance. Experimental results demonstrate that OwlCap achieves significant improvements compared to baseline models on two benchmarks: the detail-focused VDC (+4.2 Acc) and the motion-focused DREAM-1K (+4.6 F1). The HMD-270K dataset and OwlCap model will be publicly released to facilitate video captioning research community advancements.
LaQual: A Novel Framework for Automated Evaluation of LLM App Quality
Venue: arXiv cs.SE 2025
Year: 2025

LLM app stores are quickly emerging as platforms that gather a wide range of intelligent applications based on LLMs, giving users many choices for content creation, coding support, education, and more. However, the current methods for ranking and recommending apps in these stores mostly rely on static metrics like user activity and favorites, which makes it hard for users to efficiently find high-quality apps. To address these challenges, we propose LaQual, an automated framework for evaluating the quality of LLM apps. LaQual consists of three main stages: first, it labels and classifies LLM apps in a hierarchical way to accurately match them to different scenarios; second, it uses static indicators, such as time-weighted user engagement and functional capability metrics, to filter out low-quality apps; and third, it conducts a dynamic, scenario-adaptive evaluation, where the LLM itself generates scenario-specific evaluation metrics, scoring rules, and tasks for a thorough quality assessment. Experiments on a popular LLM app store show that LaQual is effective. Its automated scores are highly consistent with human judgments (with Spearman's rho of 0.62 and p=0.006 in legal consulting, and rho of 0.60 and p=0.009 in travel planning). By effectively screening, LaQual can reduce the pool of candidate LLM apps by 66.7% to 81.3%. User studies further confirm that LaQual significantly outperforms baseline systems in decision confidence, comparison efficiency (with average scores of 5.45 compared to 3.30), and the perceived value of its evaluation reports (4.75 versus 2.25). Overall, these results demonstrate that LaQual offers a scalable, objective, and user-centered solution for finding and recommending high-quality LLM apps in real-world use cases.
Hypergraph Splitting-Off via Element-Connectivity Preserving Reductions
Venue: arXiv cs.DS 2025
Year: 2025

Bérczi, Chandrasekaran, Király, and Kulkarni (ICALP 2024) recently described a splitting-off procedure in hypergraphs that preserves local-connectivity and outlined some applications. In this note we give an alternative proof via element-connectivity preserving reduction operations in graphs.
PRISM: Robust VLM Alignment with Principled Reasoning for Integrated Safety in Multimodality
Venue: arXiv cs.CR 2025
Year: 2025

Safeguarding vision-language models (VLMs) is a critical challenge, as existing methods often suffer from over-defense, which harms utility, or rely on shallow alignment, failing to detect complex threats that require deep reasoning. To this end, we introduce PRISM (Principled Reasoning for Integrated Safety in Multimodality), a system2-like framework that aligns VLMs by embedding a structured, safety-aware reasoning process. Our framework consists of two key components: PRISM-CoT, a dataset that teaches safety-aware chain-of-thought reasoning, and PRISM-DPO, generated via Monte Carlo Tree Search (MCTS) to further refine this reasoning through Direct Preference Optimization to help obtain a delicate safety boundary. Comprehensive evaluations demonstrate PRISM's effectiveness, achieving remarkably low attack success rates including 0.15% on JailbreakV-28K for Qwen2-VL and 90% improvement over the previous best method on VLBreak for LLaVA-1.5. PRISM also exhibits strong robustness against adaptive attacks, significantly increasing computational costs for adversaries, and generalizes effectively to out-of-distribution challenges, reducing attack success rates to just 8.70% on the challenging multi-image MIS benchmark. Remarkably, this robust defense is achieved while preserving, and in some cases enhancing, model utility. To promote reproducibility, we have made our code, data, and model weights available at https://github.com/SaFoLab-WISC/PRISM.
Requirements Development and Formalization for Reliable Code Generation: A Multi-Agent Vision
Venue: arXiv cs.SE 2025
Year: 2025

Automated code generation has long been considered the holy grail of software engineering. The emergence of Large Language Models (LLMs) has catalyzed a revolutionary breakthrough in this area. However, existing methods that only rely on LLMs remain inadequate in the quality of generated code, offering no guarantees of satisfying practical requirements. They lack a systematic strategy for requirements development and modeling. Recently, LLM-based agents typically possess powerful abilities and play an essential role in facilitating the alignment of LLM outputs with user requirements. In this paper, we envision the first multi-agent framework for reliable code generation based on \textsc{re}quirements \textsc{de}velopment and \textsc{fo}rmalization, named \textsc{ReDeFo}. This framework incorporates three agents, highlighting their augmentation with knowledge and techniques of formal methods, into the requirements-to-code generation pipeline to strengthen quality assurance. The core of \textsc{ReDeFo} is the use of formal specifications to bridge the gap between potentially ambiguous natural language requirements and precise executable code. \textsc{ReDeFo} enables rigorous reasoning about correctness, uncovering hidden bugs, and enforcing critical properties throughout the development process. In general, our framework aims to take a promising step toward realizing the long-standing vision of reliable, auto-generated software.
Adaptive Originality Filtering: Rejection Based Prompting and RiddleScore for Culturally Grounded Multilingual Riddle Generation
Venue: arXiv cs.CL 2025
Year: 2025

Language models are increasingly tested on multilingual creativity, demanding culturally grounded, abstract generations. Standard prompting methods often produce repetitive or shallow outputs. We introduce Adaptive Originality Filtering (AOF), a prompting strategy that enforces novelty and cultural fidelity via semantic rejection. To assess quality, we propose RiddleScore, a metric combining novelty, diversity, fluency, and answer alignment. AOF improves Distinct-2 (0.915 in Japanese), reduces Self-BLEU (0.177), and raises RiddleScore (up to +57.1% in Arabic). Human evaluations confirm fluency, creativity, and cultural fit gains. However, improvements vary: Arabic shows greater RiddleScore gains than Distinct-2; Japanese sees similar changes. Though focused on riddles, our method may apply to broader creative tasks. Overall, semantic filtering with composite evaluation offers a lightweight path to culturally rich generation without fine-tuning.
Rethinking Caching for LLM Serving Systems: Beyond Traditional Heuristics
Venue: arXiv cs.DB 2025
Year: 2025

Serving Large Language Models (LLMs) at scale requires meeting strict Service Level Objectives (SLOs) under severe computational and memory constraints. Nevertheless, traditional caching strategies fall short: exact-matching and prefix caches neglect query semantics, while state-of-the-art semantic caches remain confined to traditional intuitions, offering little conceptual departure. Building on this, we present SISO, a semantic caching system that redefines efficiency for LLM serving. SISO introduces centroid-based caching to maximize coverage with minimal memory, locality-aware replacement to preserve high-value entries, and dynamic thresholding to balance accuracy and latency under varying workloads. Across diverse datasets, SISO delivers up to 1.71$\times$ higher hit ratios and consistently stronger SLO attainment compared to state-of-the-art systems.
M3HG: Multimodal, Multi-scale, and Multi-type Node Heterogeneous Graph for Emotion Cause Triplet Extraction in Conversations
Venue: arXiv cs.CL 2025
Year: 2025

Emotion Cause Triplet Extraction in Multimodal Conversations (MECTEC) has recently gained significant attention in social media analysis, aiming to extract emotion utterances, cause utterances, and emotion categories simultaneously. However, the scarcity of related datasets, with only one published dataset featuring highly uniform dialogue scenarios, hinders model development in this field. To address this, we introduce MECAD, the first multimodal, multi-scenario MECTEC dataset, comprising 989 conversations from 56 TV series spanning a wide range of dialogue contexts. In addition, existing MECTEC methods fail to explicitly model emotional and causal contexts and neglect the fusion of semantic information at different levels, leading to performance degradation. In this paper, we propose M3HG, a novel model that explicitly captures emotional and causal contexts and effectively fuses contextual information at both inter- and intra-utterance levels via a multimodal heterogeneous graph. Extensive experiments demonstrate the effectiveness of M3HG compared with existing state-of-the-art methods. The codes and dataset are available at https://github.com/redifinition/M3HG.
CAC-CoT: Connector-Aware Compact Chain-of-Thought for Efficient Reasoning Data Synthesis Across Dual-System Cognitive Tasks
Venue: arXiv cs.AI 2025
Year: 2025

Long chain-of-thought (CoT) prompting helps Large Language Models (LLMs) solve difficult problems, but very long traces often slow or even degrade performance on fast, intuitive "System-1" tasks. We introduce Connector-Aware Compact CoT (CAC-CoT) -- a method that deliberately restricts reasoning to a small, fixed set of connector phrases, steering the model toward concise and well -- structured explanations. Despite its simplicity, our synthetic method with general-purpose LLMs yields a high-quality training quality. CAC-CoT achieves approximately 85% on GSM8K and approximately 40% on GPQA (System-2) while also achieving approximately 85% on S1-Bench (System-1), surpassing the baseline by over 20%. Its reasoning traces average approximately 300 tokens(ART), about one-third the length of baseline traces, delivering higher efficiency without loss of accuracy.